Why is this an issue?

Storing a value inside a collection at a given key or index and then unconditionally overwriting it without reading the initial value is a case of a "dead store".

$someArray[1] = "someValue";
$someArray[1] = "someOtherValue"; // Noncompliant

This practice is redundant and will cause confusion for the reader. More importantly, it is often an error and not what the developer intended to do.